Azolla filiculoides L. as a source of metal-tolerant microorganisms

Abstract

The metal hyperaccumulator Azolla filiculoides is accompanied by a microbiome potentially supporting plant during exposition to heavy metals. We hypothesized that the microbiome exposition to selected heavy metals will reveal metal tolerant strains. We used Next Generation Sequencing technique to identify possible metal tolerant strains isolated from the metal-treated plant (Pb, Cd, Cr(VI), Ni, Au, Ag). The main dominants were Cyanobacteria and Proteobacteria constituting together more than 97% of all reads. Metal treatment led to changes in the composition of the microbiome and showed significantly higher richness in the Pb-, Cd- and Cr-treated plant in comparison with other (95-105 versus 36-44). In these treatments the share of subdominant Actinobacteria (0.4-0.8%), Firmicutes (0.5-0.9%) and Bacteroidetes (0.2-0.9%) were higher than in non-treated plant (respectively: 0.02, 0.2 and 0.001%) and Ni-, Au- and Ag-treatments (respectively: <0.4%, <0.2% and up to 0.2%). The exception was Au-treatment displaying the abundance 1.86% of Bacteroidetes. In addition, possible metal tolerant genera, namely: Acinetobacter, Asticcacaulis, Anabaena, Bacillus, Brevundimonas, Burkholderia, Dyella, Methyloversatilis, Rhizobium and Staphylococcus, which form the core microbiome, were recognized by combining their abundance in all samples with literature data. Additionally, the presence of known metal tolerant genera was confirmed: Mucilaginibacter, Pseudomonas, Mycobacterium, Corynebacterium, Stenotrophomonas, Clostridium, Micrococcus, Achromobacter, Geobacter, Flavobacterium, Arthrobacter and Delftia. We have evidenced that A. filiculoides possess a microbiome whose representatives belong to metal-resistant species which makes the fern the source of biotechnologically useful microorganisms for remediation processes.

Fig 1. The relative abundance of bacteria at the phylum level across all samples.

Fig 2. Decomposition of proteobacteria on 4 classes in analysed samples.

Fig 3. The main dominant genera of proteobacteria separated into α- (blue), β- (yellow), δ- (brown) and γ-classes (green).

Violet color represents rare (<1%) 58 genera from all classes grouped together (S1–S4 Tables) and in red all unclassified microorganisms (22 families)–S5 Table.

Fig 4. The main genera dominants within bacteroidetes.

The ‘Other’ group represents those with abundance <10%.

Fig 5. The main genera dominants within firmicutes.

The group ‘Other’ represents those with abundance <10%.

Fig 6. The main genera dominants within actinobacteria.

Group ‘Other’ represents those with abundance <10%.

Fig 7. The composition of rare phyla and corresponding genera of the ‘Other’ cluster.

Fig 8. Results of PCA for studied samples.